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| Status |
Public on Aug 11, 2009 |
| Title |
Nucleosome deposition and DNA methylation at coding region boundaries |
| Organism |
Homo sapiens |
| Experiment type |
Methylation profiling by high throughput sequencing
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| Summary |
We profiled CpG methylation for human T cells and compared this pattern with public T cell nucleosome (H2A.Z) and polymerase II profiles (SRA000234). Focusing on DNA regions surrounding the start codon and stop codon, instead of the transcription start and end sites, we discovered a very intriguing pattern, namely methylation and nucleosomal peaks at those regions, more prominent than peaks near transcript boundaries. Elongating polymerases tend to pause near both coding ends immediately upstream of the epigenetic peaks, causing a significant reduction in elongation efficiency, suggesting their role in control of RNA splicing. Conserved features in underlying protein coding sequences seem to dictate their evolutionary conservation across multiple species. The nucleosomal and methylation marks are commonly associated with high sequence-encoded DNA-bending propensity but differentially with CpG density.
Keywords: Epigenetics
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| Overall design |
Sample submission examines CpG methylation from human T cells.
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| Contributor(s) |
Choi JK, Kim YJ |
| Citation(s) |
19723310, 20602769 |
| Submission date |
Aug 07, 2009 |
| Last update date |
May 15, 2019 |
| Contact name |
Jung Kyoon Choi |
| E-mail(s) |
jungkyoon@gmail.com
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| Organization name |
Genome Institute of Singapore
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| Street address |
60 Biopolis Street
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| City |
Singapore |
| ZIP/Postal code |
138672 |
| Country |
Singapore |
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| Platforms (1) |
| GPL9052 |
Illumina Genome Analyzer (Homo sapiens) |
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| Samples (1) |
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| Relations |
| SRA |
SRP001352 |
| BioProject |
PRJNA118651 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE17554_RAW.tar |
227.2 Mb |
(http)(custom) |
TAR (of BED) |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
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